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‎.circleci/config.yml

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@@ -389,7 +389,7 @@ jobs:
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sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
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sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
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fmriprep-docker -i poldracklab/fmriprep:latest \
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-e FMRIPREP_DEV 1 \
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--sloppy --write-graph --mem_mb 4096 \
@@ -408,7 +408,7 @@ jobs:
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sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
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sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
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fmriprep-docker -i poldracklab/fmriprep:latest \
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-e FMRIPREP_DEV 1 \
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
@@ -437,7 +437,7 @@ jobs:
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command: |
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rm /tmp/data/ds005/sub-01/func/*_run-01_*
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fmriprep-docker -i poldracklab/fmriprep:latest \
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-e FMRIPREP_DEV 1 \
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
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/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \

‎.circleci/ds005_outputs.txt

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11
fmriprep
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fmriprep/dataset_description.json
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fmriprep/desc-aparcaseg_dseg.tsv
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fmriprep/desc-aseg_dseg.tsv
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
@@ -9,7 +11,9 @@ fmriprep/sub-01
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fmriprep/sub-01/anat
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fmriprep/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.json
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
@@ -27,7 +31,9 @@ fmriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
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fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
@@ -48,13 +54,17 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.f
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
@@ -70,13 +80,17 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R.f
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives

‎.circleci/ds005_partial_outputs.txt

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fmriprep
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fmriprep/dataset_description.json
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fmriprep/desc-aparcaseg_dseg.tsv
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fmriprep/desc-aseg_dseg.tsv
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
@@ -9,7 +11,9 @@ fmriprep/sub-01
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fmriprep/sub-01/anat
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fmriprep/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.json
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
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/tmp/ds005/derivatives_partial

‎.circleci/ds054_outputs.txt

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fmriprep/sub-100185/anat/sub-100185_desc-brain_mask.json
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fmriprep/sub-100185/anat/sub-100185_desc-preproc_T1w.json
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fmriprep/sub-100185/anat/sub-100185_dseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json
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/tmp/ds054/derivatives

‎.circleci/ds210_outputs.txt

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/tmp/ds210/derivatives

‎.zenodo.json

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{
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"title": "fMRIPrep: a robust preprocessing pipeline for functional MRI",
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"description": "<p>fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.</p>",
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"creators": [
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{
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"name": "Esteban, Oscar",
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},
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{
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"name": "Blair, Ross",
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"affiliation": "Department of Psychology, Stanford University"
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"affiliation": "Department of Psychology, Stanford University",
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"orcid": "0000-0003-3007-1056"
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},
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{
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"name": "Markiewicz, Christopher J.",
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"affiliation": "University College London",
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"orcid": "0000-0002-9699-9052"
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},
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{
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"name": "Halchenko, Yaroslav O.",
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"affiliation": "Dartmouth College: Hanover, NH, United States",
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"orcid": "0000-0003-3456-2493"
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},
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{
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"name": "Ciric, Rastko",
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"affiliation": "Stanford University",
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"fMRI",
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"BIDS"
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],
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"related_identifiers": [
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{
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"identifier": "https://fmriprep.org",
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"relation": "documents",
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"scheme": "url"
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},
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{
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"identifier": "10.1038/s41592-018-0235-4",
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"relation": "isPartOf",
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"scheme": "doi"
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}
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],
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"license": "BSD-3-Clause",
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"upload_type": "software"
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}

‎CHANGES.rst

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1.3.2 (March 18, 2019)
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============================
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A new release providing better support for BIDS-Derivatives, an wrapping-up all the developments around TemplateFlow and stability of singularity images. With thanks to @sarenseeley for contributions.
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* ENH: Write derivatives metadata (#1546) @oesteban
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* DOC: Indicate that interpolation is NN above the EPI-to-T1w reportlet (#1542) @sarenseeley
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1.3.1.post2 (March 13, 2019)
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============================
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A hotfix release addressing issues related to TemplateFlow for Singularity users, via pinning templateflow>=0.1.2.
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1.3.1.post1 (March 11, 2019)
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============================
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A hotfix release addressing issues related to TemplateFlow for Singularity users.
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* FIX: Make sure ``--cifti-output`` requires at least one of ``fsaverage{5,6}`` (#1514) @oesteban
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* FIX: Avoid using ``$HOME`` for storing templates (#1529) @chrisfilo
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1.3.1 (March 6, 2019)
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=====================
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Updated ecosystem's versions (TemplateFlow 0.1.x, Niworkflows 0.8.x, and sMRIPrep 0.1.x)
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to include latest improvements (bugfixes from niworkflows and the new pybids interface
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of templateflow).
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TemplateFlow 0.1.0 does not require datalad anymore.
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With thanks to @franklin-feingold for contributions.
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* UX: Reduce warning levels (#1513) @effigies
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* DOC: ``fmriprep-docker`` documentation (#1515) @franklin-feingold
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* REL: 1.3.1 (#1527) @oesteban
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1.3.0.post3 (March 1, 2019)
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===========================
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Hotfix release intended for Docker users, smoothing the experience of TemplateFlow
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when using the ``-u UID`` flag is necessary.
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* [FIX] Orientation problem with niworkflows<0.7.2 (poldracklab/niworkflows#312) @effigies
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* [ENH] TemplateFlow + ``docker run -u ...`` (#1525) @oesteban
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* [ENH] Include repetition time in functional summary (#1508) @wiheto
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* [FIX] Do not crash if all aroma components are classified as noise (#1467) @jdkent
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1.3.0.post2 (February 14, 2019)
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===============================
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Hotfix release intended for Singularity users, amending the previous iteration
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that didn't fix the problem (#1510) @effigies.
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1.3.0.post1 (February 8, 2019)
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==============================
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Hotfix release intended for Singularity users. For further detail, please see
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Hotfix release intended for Singularity users. For further detail, please see
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`#1500 <https://github.com/poldracklab/fmriprep/issues/1500>`__.
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1.3.0 (February 7, 2019)
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========================
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We start the 1.3.x series including a few bugfixes, housekeeping duty and a refactors
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to leverage `sMRIPrep <https://github.com/poldracklab/smriprep>`__ (which is a fork of
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fMRIPrep's anatomical workflow), pybids>=0.7 for querying dataset, and
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fMRIPrep's anatomical workflow), pybids>=0.7 for querying dataset, and
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`TemplateFlow <https://github.com/templateflow>`__ for handling standard spaces.
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* [FIX] Bad ``fsnative`` replacement in CIfTI workflow (#1476) @oesteban
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1.2.4 (December 3, 2018)
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========================
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Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates
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Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates
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(with thanks to @emdupre).
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* [ENH] Update ME-EPI workflow to create optimal combination (#1263) @emdupre
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* [TST] Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
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* [TST] Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
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* [MAINT] Ignore project settings files from popular python/code editors (#1336) @jdkent
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* [CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies
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* [CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies
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1.1.8 (October 4, 2018)
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=======================

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